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java.lang.Objectuk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
public class SimpleArg
class for objects containing the command line arguments. Input files used have to be in EMBL format.
Field Summary | |
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private java.lang.String |
annotatedTrainSet
annotation of training set (for acp calculation) |
private java.lang.String |
blastFile
blast file which is used for evidence of correct predictions (EMBL format). |
private java.lang.String |
cDNAFile
cDNA file which is used for evidence of correct predictions (EMBL format). |
private boolean |
considerCDnaStrand
switch for strand consideration of cDNA. |
private int |
debug
debugging mode. |
private java.lang.String |
filename
filename of output file. |
private boolean |
fileOfRemovedGms
switch for output of a file containt all removed genemodels as well as a file of each analysis level with the removed genemodels. |
private int |
fuzzyBoundaries
allowed difference between genemodel and cDNA splice site to be assigned as correct splice site. |
private java.util.ArrayList |
predictedTrainSet
predictions of training set (for acp calculation). |
private java.util.ArrayList |
predictions
predictions which will be collapsed into one (EMBL format). |
Constructor Summary | |
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SimpleArg(java.lang.String[] args)
constructor of SimpleArg objects. |
Method Summary | |
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private void |
checkArguments()
method which checks arguments (briefly) |
boolean |
doConsiderCDnaStrand()
accessor method which returns switch for cDNA strand consideration. |
boolean |
doFileOfRemovedGms()
accessor method returns switch whether removed genemodels should be saved to file or not. |
private void |
doHelp(int returnValue)
Stub for providing help on usage |
org.biojava.bio.seq.Sequence |
getAnnotatedTrainSet_Sequence()
accessor method which returns a sequence object of the annotated training set, used filename is stored in attribute 'annotatedTrainSet' , retrieved from command-line argument (-a) |
java.lang.String |
getAnnotatedTrainSet()
accessor method which returns the filename of the annotated training set file stored in attribute 'annotatedTrainSet', retrieved from command-line argument (-a) |
java.lang.String |
getBlastFile()
accessor method which returns an blast filename, retrieved from command-line argument (-b) |
java.lang.String |
getCDNAFile()
accessor method which returns an cDNA filename, retrieved from command-line argument (-c) |
int |
getDebug()
accessor method which returns debug mode (int variable). |
int |
getFuzzyBoundariesValue()
accessor method which returns the value of tolerance inbetween cDNA and genemodel splice sites. |
java.lang.String |
getOutputFilename()
accessor method which returns an output filename, retrieved from command-line argument (-f) |
java.util.ArrayList |
getPredictedTrainSet_Sequences()
accessor method which returns an array list of sequence objects containing predictions on the training set of different gene predicters, used filename are stored in attribute 'predictedTrainSet' , retrieved from command-line argument (-t) |
java.util.ArrayList |
getPredictedTrainSet()
accessor method which returns an array list of filenames of predictions from different gene prediction programs on the training set, retrieved from command-line argument (-t) |
java.util.ArrayList |
getPredictions_Sequences()
accessor method which returns an array list of sequence objects containing predictions of different gene predicters, used filename are stored in attribute 'predictions' , retrieved from command-line argument (-p) |
java.util.ArrayList |
getPredictions()
accessor method which returns an array list of filenames of predictions, stored in attribute 'predictions', retrieved from command-line argument (-p) |
private void |
setArguments(java.lang.String[] _args)
method which retrieves command line arguments and saves them. |
private java.util.ArrayList |
strArrToArrList(java.lang.String[] strArr)
method which converts String[] into an ArrayList |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private java.lang.String annotatedTrainSet
private java.util.ArrayList predictedTrainSet
private java.util.ArrayList predictions
private java.lang.String blastFile
private java.lang.String cDNAFile
private int debug
private java.lang.String filename
private boolean fileOfRemovedGms
private boolean considerCDnaStrand
private int fuzzyBoundaries
Constructor Detail |
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public SimpleArg(java.lang.String[] args)
args
- command line arguments from main methodMethod Detail |
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private void setArguments(java.lang.String[] _args)
_args
- private void doHelp(int returnValue)
returnValue
- private java.util.ArrayList strArrToArrList(java.lang.String[] strArr)
strArr
- String[]
private void checkArguments()
public java.lang.String getAnnotatedTrainSet()
public org.biojava.bio.seq.Sequence getAnnotatedTrainSet_Sequence()
public java.util.ArrayList getPredictedTrainSet()
public java.util.ArrayList getPredictedTrainSet_Sequences()
public java.util.ArrayList getPredictions()
public java.util.ArrayList getPredictions_Sequences()
public int getDebug()
Debug
public java.lang.String getBlastFile()
public java.lang.String getCDNAFile()
public java.lang.String getOutputFilename()
public boolean doFileOfRemovedGms()
public int getFuzzyBoundariesValue()
public boolean doConsiderCDnaStrand()
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